1 |
#include <iostream> |
2 |
#include <cstdlib> |
3 |
|
4 |
#ifdef IS_MPI |
5 |
#include "mpiSimulation.hpp" |
6 |
#include <unistd.h> |
7 |
#endif //is_mpi |
8 |
|
9 |
#include "Integrator.hpp" |
10 |
#include "simError.h" |
11 |
|
12 |
|
13 |
Symplectic::Symplectic( SimInfo* theInfo, ForceFields* the_ff ){ |
14 |
|
15 |
info = theInfo; |
16 |
myFF = the_ff; |
17 |
isFirst = 1; |
18 |
|
19 |
molecules = info->molecules; |
20 |
nMols = info->n_mol; |
21 |
|
22 |
// give a little love back to the SimInfo object |
23 |
|
24 |
if( info->the_integrator != NULL ) delete info->the_integrator; |
25 |
info->the_integrator = this; |
26 |
|
27 |
// check for constraints |
28 |
|
29 |
constrainedI = NULL; |
30 |
constrainedJ = NULL; |
31 |
constrainedDsqr = NULL; |
32 |
nConstrained = 0; |
33 |
|
34 |
checkConstraints(); |
35 |
} |
36 |
|
37 |
Symplectic::~Symplectic() { |
38 |
|
39 |
if( nConstrained ){ |
40 |
delete[] constrainedI; |
41 |
delete[] constrainedJ; |
42 |
delete[] constrainedDsqr; |
43 |
} |
44 |
|
45 |
} |
46 |
|
47 |
void Symplectic::checkConstraints( void ){ |
48 |
|
49 |
|
50 |
isConstrained = 0; |
51 |
|
52 |
Constraint *temp_con; |
53 |
Constraint *dummy_plug; |
54 |
temp_con = new Constraint[info->n_SRI]; |
55 |
nConstrained = 0; |
56 |
int constrained = 0; |
57 |
|
58 |
SRI** theArray; |
59 |
for(int i = 0; i < nMols; i++){ |
60 |
|
61 |
theArray = (SRI**) molecules[i].getMyBonds(); |
62 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
63 |
|
64 |
constrained = theArray[j]->is_constrained(); |
65 |
|
66 |
if(constrained){ |
67 |
|
68 |
dummy_plug = theArray[j]->get_constraint(); |
69 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
70 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
71 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
72 |
|
73 |
nConstrained++; |
74 |
constrained = 0; |
75 |
} |
76 |
} |
77 |
|
78 |
theArray = (SRI**) molecules[i].getMyBends(); |
79 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
80 |
|
81 |
constrained = theArray[j]->is_constrained(); |
82 |
|
83 |
if(constrained){ |
84 |
|
85 |
dummy_plug = theArray[j]->get_constraint(); |
86 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
87 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
88 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
89 |
|
90 |
nConstrained++; |
91 |
constrained = 0; |
92 |
} |
93 |
} |
94 |
|
95 |
theArray = (SRI**) molecules[i].getMyTorsions(); |
96 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
97 |
|
98 |
constrained = theArray[j]->is_constrained(); |
99 |
|
100 |
if(constrained){ |
101 |
|
102 |
dummy_plug = theArray[j]->get_constraint(); |
103 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
104 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
105 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
106 |
|
107 |
nConstrained++; |
108 |
constrained = 0; |
109 |
} |
110 |
} |
111 |
} |
112 |
|
113 |
if(nConstrained > 0){ |
114 |
|
115 |
isConstrained = 1; |
116 |
|
117 |
if(constrainedI != NULL ) delete[] constrainedI; |
118 |
if(constrainedJ != NULL ) delete[] constrainedJ; |
119 |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
120 |
|
121 |
constrainedI = new int[nConstrained]; |
122 |
constrainedJ = new int[nConstrained]; |
123 |
constrainedDsqr = new double[nConstrained]; |
124 |
|
125 |
for( int i = 0; i < nConstrained; i++){ |
126 |
|
127 |
constrainedI[i] = temp_con[i].get_a(); |
128 |
constrainedJ[i] = temp_con[i].get_b(); |
129 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
130 |
} |
131 |
} |
132 |
|
133 |
delete[] temp_con; |
134 |
} |
135 |
|
136 |
|
137 |
void Symplectic::integrate( void ){ |
138 |
|
139 |
int i, j; // loop counters |
140 |
int nAtoms = info->n_atoms; // the number of atoms |
141 |
double kE = 0.0; // the kinetic energy |
142 |
double rot_kE; |
143 |
double trans_kE; |
144 |
int tl; // the time loop conter |
145 |
double dt2; // half the dt |
146 |
|
147 |
double vx, vy, vz; // the velocities |
148 |
double vx2, vy2, vz2; // the square of the velocities |
149 |
double rx, ry, rz; // the postitions |
150 |
|
151 |
double ji[3]; // the body frame angular momentum |
152 |
double jx2, jy2, jz2; // the square of the angular momentums |
153 |
double Tb[3]; // torque in the body frame |
154 |
double angle; // the angle through which to rotate the rotation matrix |
155 |
double A[3][3]; // the rotation matrix |
156 |
double press[9]; |
157 |
|
158 |
int time; |
159 |
|
160 |
double dt = info->dt; |
161 |
double runTime = info->run_time; |
162 |
double sampleTime = info->sampleTime; |
163 |
double statusTime = info->statusTime; |
164 |
double thermalTime = info->thermalTime; |
165 |
|
166 |
int n_loops = (int)( runTime / dt ); |
167 |
int sample_n = (int)( sampleTime / dt ); |
168 |
int status_n = (int)( statusTime / dt ); |
169 |
int vel_n = (int)( thermalTime / dt ); |
170 |
|
171 |
int calcPot, calcStress; |
172 |
int isError; |
173 |
|
174 |
tStats = new Thermo( info ); |
175 |
e_out = new StatWriter( info ); |
176 |
dump_out = new DumpWriter( info ); |
177 |
|
178 |
Atom** atoms = info->atoms; |
179 |
DirectionalAtom* dAtom; |
180 |
dt2 = 0.5 * dt; |
181 |
|
182 |
// initialize the forces before the first step |
183 |
|
184 |
myFF->doForces(1,1); |
185 |
|
186 |
if( info->setTemp ){ |
187 |
|
188 |
tStats->velocitize(); |
189 |
} |
190 |
|
191 |
dump_out->writeDump( 0.0 ); |
192 |
e_out->writeStat( 0.0 ); |
193 |
|
194 |
calcPot = 0; |
195 |
|
196 |
for( tl=0; tl<nLoops; tl++){ |
197 |
|
198 |
integrateStep( calcPot, calcStress ); |
199 |
|
200 |
time = tl + 1; |
201 |
|
202 |
if( info->setTemp ){ |
203 |
if( !(time % vel_n) ) tStats->velocitize(); |
204 |
} |
205 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
206 |
if( !((time+1) % status_n) ) { |
207 |
calcPot = 1; |
208 |
calcStress = 1; |
209 |
} |
210 |
if( !(time % status_n) ){ |
211 |
e_out->writeStat( time * dt ); |
212 |
calcPot = 0; |
213 |
if (!strcasecmp(info->ensemble, "NPT")) calcStress = 1; |
214 |
else calcStress = 0; |
215 |
} |
216 |
|
217 |
|
218 |
} |
219 |
|
220 |
dump_out->writeFinal(); |
221 |
|
222 |
delete dump_out; |
223 |
delete e_out; |
224 |
} |
225 |
|
226 |
|
227 |
void Symplectic::moveA( void ){ |
228 |
|
229 |
int i,j,k; |
230 |
int atomIndex, aMatIndex; |
231 |
DirectionalAtom* dAtom; |
232 |
double Tb[3]; |
233 |
double ji[3]; |
234 |
|
235 |
for( i=0; i<nAtoms; i++ ){ |
236 |
atomIndex = i * 3; |
237 |
aMatIndex = i * 9; |
238 |
|
239 |
// velocity half step |
240 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
241 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
242 |
|
243 |
// position whole step |
244 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
245 |
pos[j] += dt * vel[j]; |
246 |
|
247 |
|
248 |
if( atoms[i]->isDirectional() ){ |
249 |
|
250 |
dAtom = (DirectionalAtom *)atoms[i]; |
251 |
|
252 |
// get and convert the torque to body frame |
253 |
|
254 |
Tb[0] = dAtom->getTx(); |
255 |
Tb[1] = dAtom->getTy(); |
256 |
Tb[2] = dAtom->getTz(); |
257 |
|
258 |
dAtom->lab2Body( Tb ); |
259 |
|
260 |
// get the angular momentum, and propagate a half step |
261 |
|
262 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
263 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
264 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
265 |
|
266 |
// use the angular velocities to propagate the rotation matrix a |
267 |
// full time step |
268 |
|
269 |
// rotate about the x-axis |
270 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
271 |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
272 |
|
273 |
// rotate about the y-axis |
274 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
275 |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
276 |
|
277 |
// rotate about the z-axis |
278 |
angle = dt * ji[2] / dAtom->getIzz(); |
279 |
this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
280 |
|
281 |
// rotate about the y-axis |
282 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
283 |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
284 |
|
285 |
// rotate about the x-axis |
286 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
287 |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
288 |
|
289 |
dAtom->setJx( ji[0] ); |
290 |
dAtom->setJy( ji[1] ); |
291 |
dAtom->setJz( ji[2] ); |
292 |
} |
293 |
|
294 |
} |
295 |
} |
296 |
|
297 |
|
298 |
void Integrator::moveB( void ){ |
299 |
int i,j,k; |
300 |
int atomIndex; |
301 |
DirectionalAtom* dAtom; |
302 |
double Tb[3]; |
303 |
double ji[3]; |
304 |
|
305 |
for( i=0; i<nAtoms; i++ ){ |
306 |
atomIndex = i * 3; |
307 |
|
308 |
// velocity half step |
309 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
310 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
311 |
|
312 |
if( atoms[i]->isDirectional() ){ |
313 |
|
314 |
dAtom = (DirectionalAtom *)atoms[i]; |
315 |
|
316 |
// get and convert the torque to body frame |
317 |
|
318 |
Tb[0] = dAtom->getTx(); |
319 |
Tb[1] = dAtom->getTy(); |
320 |
Tb[2] = dAtom->getTz(); |
321 |
|
322 |
dAtom->lab2Body( Tb ); |
323 |
|
324 |
// get the angular momentum, and complete the angular momentum |
325 |
// half step |
326 |
|
327 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
328 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
329 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
330 |
|
331 |
jx2 = ji[0] * ji[0]; |
332 |
jy2 = ji[1] * ji[1]; |
333 |
jz2 = ji[2] * ji[2]; |
334 |
|
335 |
dAtom->setJx( ji[0] ); |
336 |
dAtom->setJy( ji[1] ); |
337 |
dAtom->setJz( ji[2] ); |
338 |
} |
339 |
} |
340 |
|
341 |
} |
342 |
|
343 |
|
344 |
void Integrator::constrainA(){ |
345 |
|
346 |
|
347 |
|
348 |
|
349 |
} |
350 |
|
351 |
|
352 |
|
353 |
|
354 |
|
355 |
|
356 |
|
357 |
|
358 |
|
359 |
void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3], |
360 |
double A[3][3] ){ |
361 |
|
362 |
int i,j,k; |
363 |
double sinAngle; |
364 |
double cosAngle; |
365 |
double angleSqr; |
366 |
double angleSqrOver4; |
367 |
double top, bottom; |
368 |
double rot[3][3]; |
369 |
double tempA[3][3]; |
370 |
double tempJ[3]; |
371 |
|
372 |
// initialize the tempA |
373 |
|
374 |
for(i=0; i<3; i++){ |
375 |
for(j=0; j<3; j++){ |
376 |
tempA[j][i] = A[i][j]; |
377 |
} |
378 |
} |
379 |
|
380 |
// initialize the tempJ |
381 |
|
382 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
383 |
|
384 |
// initalize rot as a unit matrix |
385 |
|
386 |
rot[0][0] = 1.0; |
387 |
rot[0][1] = 0.0; |
388 |
rot[0][2] = 0.0; |
389 |
|
390 |
rot[1][0] = 0.0; |
391 |
rot[1][1] = 1.0; |
392 |
rot[1][2] = 0.0; |
393 |
|
394 |
rot[2][0] = 0.0; |
395 |
rot[2][1] = 0.0; |
396 |
rot[2][2] = 1.0; |
397 |
|
398 |
// use a small angle aproximation for sin and cosine |
399 |
|
400 |
angleSqr = angle * angle; |
401 |
angleSqrOver4 = angleSqr / 4.0; |
402 |
top = 1.0 - angleSqrOver4; |
403 |
bottom = 1.0 + angleSqrOver4; |
404 |
|
405 |
cosAngle = top / bottom; |
406 |
sinAngle = angle / bottom; |
407 |
|
408 |
rot[axes1][axes1] = cosAngle; |
409 |
rot[axes2][axes2] = cosAngle; |
410 |
|
411 |
rot[axes1][axes2] = sinAngle; |
412 |
rot[axes2][axes1] = -sinAngle; |
413 |
|
414 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
415 |
|
416 |
for(i=0; i<3; i++){ |
417 |
ji[i] = 0.0; |
418 |
for(k=0; k<3; k++){ |
419 |
ji[i] += rot[i][k] * tempJ[k]; |
420 |
} |
421 |
} |
422 |
|
423 |
// rotate the Rotation matrix acording to: |
424 |
// A[][] = A[][] * transpose(rot[][]) |
425 |
|
426 |
|
427 |
// NOte for as yet unknown reason, we are setting the performing the |
428 |
// calculation as: |
429 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
430 |
|
431 |
for(i=0; i<3; i++){ |
432 |
for(j=0; j<3; j++){ |
433 |
A[j][i] = 0.0; |
434 |
for(k=0; k<3; k++){ |
435 |
A[j][i] += tempA[i][k] * rot[j][k]; |
436 |
} |
437 |
} |
438 |
} |
439 |
} |